Nuclear Dynamics: Molecular Biology and Visualization of the Nucleus PDF
Preview Nuclear Dynamics: Molecular Biology and Visualization of the Nucleus
K. Nagata, K. Takeyasu (Eds.) Nuclear Dynamics Molecular Biology and Visualization of the Nucleus K. Nagata, K. Takeyasu (Eds.) Nuclear Dynamics Molecular Biology and Visualization of the Nucleus With 48 Figures, Including 34 in Color Springer Kyosuke Nagata, Ph.D. Professor Department of Infection Biology Graduate School of Comprehensive Human Sciences University of Tsukuba Tennohdai, Tsukuba, Ibaraki 305-8575, Japan Kunio Takeyasu, Dr.Sci. Professor Laboratory of Plasma Membrane and Nuclear Signaling Kyoto University Graduate School of Biostudies Sakyo-ku, Kitashirakawa-Oiwake-cho, Kyoto 606-8502, Japan Library of Congress Control Number: 2006938399 ISBN-10 4-431-30054-6 Springer Tokyo Berlin Heidelberg New York ISBN-13 978-4-431-30054-0 Springer Tokyo Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in other ways, and storage in data banks. The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product liability: The publisher can give no guarantee for information about drug dosage and application thereof contained in this book. In every individual case the respective user must check its accuracy by consulting other pharmaceutical literature. Springer is a part of Springer Science+Business Media springer.com © Springer 2007 Printed in Japan Typesetting: Camera-ready by the editors and authors Printing and binding: Shinano, Japan Printed on acid-free paper Preface: Overview of Nuclear Organization and Nuclear Dynamics Kunio Takeyasu Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University Graduate School of Biostudies, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan In contrast to the fact that prokaryotes, which do not have cell nuclei, can live only as unicellular organisms, eukaryotes bearing cell nuclei exist as a huge variety of organisms from single cell to higher multicellular organ isms having higher-level functions. The reason for this is that cell nuclei of eukaryotes have a combination of mechanisms to store, retain, and transfer the very long genome stably and to produce cells carrying different func tions from the identical genome information. Such functions of cell nuclei are supported by the intranuclear higher-order architecture. To understand vital activities closely related to genome fiinction, such as cell prolifera tion, environment responsiveness, reproduction, development, differentia tion, and aging, it is necessary to know the fundamental structure and con struction of the cell nucleus, "a container" of genome (shown above). In this book, we investigate the dynamics of the nuclear structure as the basis supporting genome function, thereby comprehensively understanding how the higher-order structure of the nucleus is established and how it corre lates with the expression of a variety of vital activities, including cell pro liferation and ontogenesis, by combining biochemical and molecular ge netic methods with the latest imaging techniques. Nuclear Organization A cell nucleus (hereafter referred to as nucleus) is an organelle that is compartmentalized by a special membrane structure, the nuclear envelope. A nucleus has a number of structural characteristics that other organelles do not have. One of these is internal storage of genomic DNA, a chemi cally single and physically very long supermolecule. In the case of human cells, DNA approximately 2 m long is stored in a tiny nucleus with a dia meter of ~5 // m. Accurate replication and distribution of such a long VI K. Takeyasu DNA molecule is required for the cell cycle regulation, and selective tran scription of appropriate genes is necessary for transcriptional regulation. These facts conjure up an image of a highly orderly structure being re quired in a nucleus to keep and to express genome functions. The second characteristic of a nucleus is that it provides "space" for molecules such as proteins and RNAs to dissociate and distribute easily, since it is a giant organelle and lacks an internal membrane structure as a partition. In fact, many functional complexes (several kinds of nuclear bodies, such as nu clear speckle, Cajal body, and promyelocytic leukemia oncoprotein [PML] body, as well as nucleolus) exist in the nucleus (shown above), and its structure and function show dynamic alteration depending on the physi ological conditions. Such functional complexes are designated as intranu clear compartments and/or intranuclear domains according to their func tions and sizes. The third characteristic is a nuclear envelope structure, which exists as a boundary between the nucleus and the cytoplasm. Nu- clearpore complexes exist to link two lipid bilayers that constitute a nu clear envelope, and regulate the bidirectional transport between the nucle us and the cytoplasm. A mesh-like structure, known as the nuclear lamina, in the inner layer of the nuclear envelope provide the scaffolding for chromosome functions in animal cells. Thus, the nuclear envelope, includ ing nuclear pores, supports genome function of a nucleus structurally and in terms of substance transport. Preface: Overview of Nuclear Organization and Nuclear Dynamics VII Fundamental Problems to be Solved Intensive investigations of individual events in the nucleus, such as tran scription of genes, DNA replication, repair, recombination, and RNA processing, have been conducted to date. Biological factors involved in the raw process of individual vital functions have been discovered by bio chemical, molecular, biological, and genetic methods, and their molecular bases and molecular mechanisms have been analyzed. Nevertheless, how individual reactions are regulated temporally and spatially has not been investigated so intensively in spite of its importance, since most of the findings were based on in vitro reactions. The amount of intranuclear proteins is huge (several hundred mg proteins/ml, assuming that they are distributed evenly in the nucleus). These proteins function without forming precipitations in the living cells by forming highly orderly complexes with chromosomal DNAs and RNAs. However, they have not been well-investigated biochemically, since most nuclear proteins form highly insoluble precipitations as a result of biochemical treatment, including DNA degradation. Although such in soluble proteins, called nuclear matrix proteins, may potentially affect gene expression as a nuclear architecture, the function of these has not been clarified thus far due to difficulties in the biochemical analysis. Trend of New Nucleus Research Genomic sequences of a variety of living organisms have been read, and genes coding for proteins, components of organisms, are being unraveled comprehensively. The presence and function of novel proteins can be speculated on and searched for using such genome information. In addi tion, thanks to the development of proteomics technology, the protein pro file of a number of organelles in a nucleus, including the nucleolus, is now being clarified inclusively. Under the circumstances, single molecular dy namics in living cells and visualization of intermolecular binding are now enabled by great advances in the development of several fluorescent pro teins and imaging techniques as independent technologies. By expressing target proteins fused to fluorescent proteins in cells, membrane proteins as well as nuclear proteins, which have thus far been difficult to handle bio chemically, can be dynamically investigated in living cells. Based on the genome information accumulated as mentioned above, it becomes possible to map the dynamics of individual proteins in cells in a three-dimensional VIII K. Takeyasu structure, over time, by a combination of biochemical and molecular ge netic methods with molecular imaging techniques. Based on the dynamic viewpoint of time, unforeseen and unex pected findings are being revealed, including the fact that importin j3, which transports nuclear proteins into the nucleus in the intermittent phase, is also involved in spindle formation, that components of the nuclear pore complex are present in the centromere in the mitotic phase and are in volved in chromosome disjunction, and that RNAs produced as transcrip tional products transform DNA in their transcriptional regions into inactive heterochromatin. In other words, spatiotemporal changes of cellular molecules and structures in vital activity can now be captured. In addition to the progress in the technologies investigating molecular dynamics, techniques derived to analyze the genome are also advancing markedly, and it has now been found that abnormalities of nu clear proteins induce several diseases, thanks to identification of genes re sponsible for these diseases. These include "nuclear membrane diseases," which are triggered by abnormalities in nuclear envelope proteins. For in stance, a number of diseases, such as Emery-Dreifuss muscular dystrophy, familial lipodystrophy, progeria syndrome, and Pelger-Huet malformation, occur as a result of deletions and/or mutations of proteins of the inner layer of the nuclear envelope as well as nuclear lamina. The fact that nuclear envelope proteins are responsible for several diseases showing different symptoms suggests that the nuclear envelope architecture can regulate the expression of genome information dynamically, depending on the devel opmental and environmental status. Hope for Fruitful Research on Nuclear Dynamics Many authors of chapters in this book participated in the International Workshop on Nuclear Dynamics: Approaches from Biochemistry, Molecular Biology and Visual Biology at Yokohama, Japan on December 5, 2002. All of us agreed that, in order to understand vital activity closely related to genome function, it is prerequisite to understand the inner struc ture of the cell nucleus that supports the genome function. Since the struc ture is not always stable but varies from hour to hour, it is necessary to capture dynamic changes of the structure and function from the viewpoint of molecular dynamics. Since dynamic structural changes might be related to unexpected functions, researchers from a broad range of specialized ar eas including nuclear envelope, nuclear transport, chromosome structure, transcription, RNA processing, and nuclear domain structures should pro- Preface: Overview of Nuclear Organization and Nuclear Dynamics IX mote studies by collaborating organically with researchers specializing in imaging and nanotechnology. From this point of view, this book was writ ten. It took over 3 years to complete, with the tremendous efforts of indi vidual authors. We hope that the outcomes of this field are prerequisite for the understanding of gene expression, DNA replication, and chromatin struc ture, and are likely to open new avenues for the elucidation of genes re sponsible for "nuclear membrane diseases" and abnormalities in chromo somal distribution, as well as mechanisms involved in nuclear reprogramming. Study results may also support research activities aiming at applications in regenerative medicine, which include the development of artificial chromosomes used in gene therapy as well as artificial cells that have specialized nuclear functions. In this sense, nuclear dynamics re search could open up an extremely important field in terms of understand ing the basics of life. Contents Preface: Overview of Nuclear Organization and Nuclear Dynamics Kunio Takeyasu V 1. Visual Biology of Nuclear Dynamics: From Micro- to Nano-dynamics of Nuclear Components Shige H. Yoshimura 1 2. Nuclear Envelope: Nanoarray Responsive to Aldosterone Hans Oberleithner 38 3. Mitotic Chromosome Segregation Control Yu Xue, Chuanhai Fu, Yong Miao, Jianhui Yao, Zhen Dou, Jie Zhang, Larry Brako, and Xuebiao Yao 55 4. Breakdown and Reformation of the Nuclear Envelope Tokuko Haraguchi and Yasushi Hiraoka 89 5. Functional Organization and Dynamic Aspects of Nucleoli During the Cell Cycle Takuya Saiwakiand Yoshihiro Yoneda 107 6. Dynamics, Roles, and Diseases of the Nuclear Membrane, Lamins, and Lamin-binding Proteins Tsuneyoshi Horigome, Yasuhiro Hirano, and Kazuhiro Furukawa 123 7. Gene Selectors Consisting of DNA-Binding Proteins, Histones, and Histone-Binding Proteins Regulate the Three Major Stages of Gene Expression Shinsuke Muto and Masami Horikoshi 145 8. Dynamic Chromatin Loops and the Regulation of Gene Expression Hiroshi Kimura and Peter R. Cook 177 XII Contents 9. Nuclear Architecture: Topology and Function of Chromatin- and Non-Chromatin Nuclear Domains Satoshi Tashiro, Marion Cremer, Irina Solovei, and Thomas Cremer 197 10-1. Regulation of Chromatin Structure by Curved DNA: How Activator Binding Sites Become Accessible Takashi Ohyama 227 10-2. Actin-Related Proteins Involved in Nuclear and Chromatin Dynamics Masahiko Harata 239 10-3. Effects of 5-Bromodeoxyuridine on Chromatin Structure Dai Ayusawa 249 10-4. Transcriptional Modulation by Nuclear Matrix Protein P130/MAT3 Associated with MAR/SAR Yasuhide Hibino, Tatsuhiro Usui, and Koichi Hiraga 255 10-5. Breaking and Tessellating the Contiguous Nuclear Genome Kojiro Ishii 263 Perspective—toward understanding the in situ genome function Kyosuke Nagata 271 Index 277
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